Publications
Key Publications
Publications from the Krijgsveld lab:
https://pubmed.ncbi.nlm.nih.gov/?term=jeroen+krijgsveld+%5Bau%5D&sort=date&size=100
Sigismondo G, Arseni L, Hofmann TG, Seiffert M, Krijgsveld J. Multi-layered chromatin proteomics identifies cell vulnerabilities in DNA repair. Nucleic Acids Research 2023; 51(2):687-711. doi: 10.1093/nar/gkac1264.
Trendel J, Boileau E, Jochem M, Dieterich C, Krijgsveld J. PEPseq quantifies transcriptome-wide changes in protein occupancy and reveals selective translational repression after translational stress. Nucleic Acids Res. 2023; 51(14):e79. doi: 10.1093/nar/gkad557.
Sigismondo G, Papageorgiou DN, Krijgsveld J. Cracking chromatin with proteomics: From chromatome to histone modifications. Proteomics. 2022; 22(15-16):e2100206. doi: 10.1002/pmic.202100206.
Kalxdorf, M., T. Müller, O. Stegle and J. Krijgsveld. IceR improves proteome coverage and data completeness in global and single-cell proteomics. Nat Commun (2021), 12(1):4787. doi: 10.1038/s41467-021-25077-6. PMID: 34373457
Müller T, Kalxdorf M, Longuespée R, Kazdal DN, Stenzinger A, Krijgsveld J.
Automated sample preparation with SP3 for low-input clinical proteomics.
Mol Syst Biol (2020); 16(1):e9111. https://doi.org/10.15252/msb.20199111
Bunina D, Abazova N, Diaz N, Noh K-M*, Krijgsveld J*, Zaugg JB*. Genomic rewiring of SOX2 chromatin interaction network during differentiation of ESCs to postmitotic neurons. *Joint senior authors. Cell Syst (2020), 10(6):480-494.e8. https://doi.org/10.1016/j.cels.2020.05.003
Rafiee MR, Sigismondo G, Kalxdorf M, Förster L, Brügger B, Béthune J, Krijgsveld J. Protease-resistant streptavidin for interaction proteomics. Mol Syst Biol (2020), 16(5):e9370. https://doi.org/10.15252/msb.20199370
Trendel J, Schwarzl T, Horos R, Prakash A, Bateman A, Hentze MW, Krijgsveld J. The Human RNA-Binding Proteome and Its Dynamics During Arsenite-Induced Translational Arrest. Cell (2019) 176(1-2):391-403. https://doi.org/10.1016/j.cell.2018.11.004
Hughes C, Moggridge S, Müller T, Sorensen P, Morin G, and Krijgsveld J. Single-pot, solid-phase-enhanced sample preparation for proteomics experiments. Nature Protocols (2019) 14(1):68-85. https://doi.org/10.1038/s41596-018-0082-x
Rafiee MR, Girardot C, Sigismondo G, Krijgsved J. Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins. Mol Cell. (2016);64(3):624-635. (Featured article); Preview' by Tu S, LeRoy G, Reinberg D. Chromatin Starts to Come Clean. Mol Cell (2016);64(3):439-441; 'News and views' by Bensaddek D, Lamond AI. Unlocking the chromatin code by deciphering protein–DNA interactions. Mol Syst Biol (2016);12:887; 'Research Highlight' by S. Larochelle. A pluripotent approach. Nature Methods (2016);13:975
Virant-Klun I, Leicht S, Hughes C, Krijgsved J. Identification of maturation-specific proteins by single-cell proteomics of human oocytes. Mol Cell Proteomics. (2016), 15(8):2616-27
Haas S, Hansson J, Klimmeck D, Loeffler D, Velten L, Uckelmann H, Wurzer S, Prendergast AM, Schnell A, Hexel K, Santarella-Mellwig R, Blaszkiewicz S, Kuck A, Geiger H, Milsom MD, Steinmetz LM, Schroeder T, Trumpp A, Krijgsved J, Essers MA. Inflammation-Induced Emergency Megakaryopoiesis Driven by Hematopoietic Stem Cell-like Megakaryocyte Progenitors. Cell Stem Cell. (2015), 17(4):422-34
Hughes C, Foehr S, Garfield DA, Furlong EE, Steinmetz LM, Krijgsved J. Ultrasensitive proteome analysis using paramagnetic bead technology. Molecular Systems Biology (2014); 10: 757 'News and Views' by Kanshin and Thibault, Molecular Systems Biology (2014); 10: 758
Eichelbaum K, Winter M, Diaz MB, Herzig S, Krijgsved J (2012). Selective enrichment of newly synthesized proteins for quantitative secretome analysis. Nature Biotechnology 30(10):984-90
Hansson J, Rafiee MR, Reiland S, Polo JM, Gehring J, Okawa S, Huber W, Hochedlinger K, Krijgsved J (2012). Highly coordinated proteome dynamics during reprogramming of somatic cells to pluripotency. Cell Reports 2(6):1579-92
Castello A, Fischer B, Schuschke K, Horos R, Beckmann B, Strein C, Humphreys DT, Preiss T, Steinmetz L, Krijgsved J* and Hentze MW* (2012). Insights into RNA biology from a mammalian cell mRNA interactome. Cell 149(6):1393-406. *Joint last author
D. Van Hoof, J. Muñoz, S.R. Braam, M.W.H. Pinkse, R. Linding, A.J.R. Heck, C.L. Mummery, and Krijgsved J. Phosphorylation dynamics during early differentiation of human embryonic stem cells (2009). Cell Stem Cell 5(2): 214-226
All publications (2012 - present)
Publications from the Krijgsveld lab:
https://pubmed.ncbi.nlm.nih.gov/?term=jeroen+krijgsveld+%5Bau%5D&sort=date&size=100
2023
Sigismondo G, Arseni L, Hofmann TG, Seiffert M, Krijgsveld J. Multi-layered chromatin proteomics identifies cell vulnerabilities in DNA repair. Nucleic Acids Research 2023; 51(2):687-711. doi: 10.1093/nar/gkac1264.
Müller T, Cremonini MA, Kliewer G, Krijgsveld J. Automated Sample Preparation for Mass Spectrometry-Based Clinical Proteomics. Methods Mol Biol. 2023; 2718:181-211. doi: 10.1007/978-1-0716-3457-8_11.
Trendel J, Boileau E, Jochem M, Dieterich C, Krijgsveld J. PEPseq quantifies transcriptome-wide changes in protein occupancy and reveals selective translational repression after translational stress. Nucleic Acids Res. 2023; 51(14):e79. doi: 10.1093/nar/gkad557.
Weidenauer K, Schmidt C, Rohde C, Pauli C, Blank MF, Heid D, Waclawiczek A, Corbacioglu A, Göllner S, Lotze M, Vierbaum L, Renders S, Krijgsveld J, Raffel S, Sauer T, Trumpp A, Pabst C, Müller-Tidow C, Janssen M. The ribosomal protein S6 kinase alpha-1 (RPS6KA1) induces resistance to venetoclax/azacitidine in acute myeloid leukemia. Leukemia. 2023 Aug;37(8):1611-1625. doi: 10.1038/s41375-023-01951-8.
Schäfer M, Schneider M, Müller T, Franz N, Braspenning-Wesch I, Stephan S, Schmidt G, Krijgsveld J, Helm D, Rösl F, Hasche D. Spatial tissue proteomics reveals distinct landscapes of heterogeneity in cutaneous papillomavirus-induced keratinocyte carcinomas. J Med Virol. 2023; 95(6):e28850. doi: 10.1002/jmv.28850.
Fatti E, Hirth A, Švorinić A, Günther M, Stier G, Cruciat CM, Acebrón SP, Papageorgiou D, Sinning I, Krijgsveld J, Höfer T, Niehrs C. DEAD box RNA helicases act as nucleotide exchange factors for casein kinase 2. Sci Signal. 2023;16(782):eabp8923. doi: 10.1126/scisignal.abp8923.
Francois L, Boskovic P, Knerr J, He W, Sigismondo G, Schwan C, More TH, Schlotter M, Conway ME, Krijgsveld J, Hiller K, Grosse R, Lichter P, Radlwimmer B. BCAT1 redox function maintains mitotic fidelity. Cell Rep. 2023; 42(3):112217. doi: 10.1016/j.celrep.2023.112217.
Weigel B, Tegethoff JF, Grieder SD, Lim B, Nagarajan B, Liu YC, Truberg J, Papageorgiou D, Adrian-Segarra JM, Schmidt LK, Kaspar J, Poisel E, Heinzelmann E, Saraswat M, Christ M, Arnold C, Ibarra IL, Campos J, Krijgsveld J, Monyer H, Zaugg JB, Acuna C, Mall M.MYT1L haploinsufficiency in human neurons and mice causes autism-associated phenotypes that can be reversed by genetic and pharmacologic intervention. Mol Psychiatry. 2023 doi: 10.1038/s41380-023-01959-7. Online ahead of print.
Vit G, Hirth A, Neugebauer N, Kraft BN, Sigismondo G, Cazzola A, Tessmer C, Duro J, Krijgsveld J, Hofmann I, Berger M, Klüter H, Niehrs C, Nilsson J, Krämer A. Human SLFN5 and its Xenopus Laevis ortholog regulate entry into mitosis and oocyte meiotic resumption. Cell Death Discov. 2022; 8(1):484. doi: 10.1038/s41420-022-01274-0
2022
Gegner HM, Naake T, Dugourd A, Müller T, Czernilofsky F, Kliewer G, Jäger E, Helm B, Kunze-Rohrbach N, Klingmüller U, Hopf C, Müller-Tidow C, Dietrich S, Saez-Rodriguez J, Huber W, Hell R, Poschet G, Krijgsveld J. Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis. Front Mol Biosci. 2022; 9:961448. doi: 10.3389/fmolb.2022.961448.
Sigismondo G, Papageorgiou DN, Krijgsveld J. Cracking chromatin with proteomics: From chromatome to histone modifications. Proteomics. 2022; 22(15-16):e2100206. doi: 10.1002/pmic.202100206.
Francois L, Boskovic P, Knerr J, He W, Sigismondo G, Schwan C, More TH, Schlotter M, Krijgsveld J, Hiller K, Grosse R, Lichter P, Radlwimmer B. BCAT1 redox function maintains mitotic fidelity. Cell Rep. 2022; 41(3):111524. doi: 10.1016/j.celrep.2022.111524.
Zhou F, Aroua N, Liu Y, Rohde C, Cheng J, Wirth AK, Fijalkowska D, Göllner S, Lotze M, Yun H, Yu X, Pabst C, Sauer T, Oellerich T, Serve H, Rollig C, Bornhauser M, Thiede C, Baldus C, Frye M, Raffel S, Krijgsveld J, Jeremias I, Beckmann R, Trumpp A, Muller-Tidow C. A dynamic rRNA ribomethylome drives stemness in acute myeloid leukemia. Cancer Discov. 2022; 13(2):332-347. doi: 10.1158/2159-8290.CD-22-0210
Allert C, Waclawiczek A, Zimmermann SMN, Göllner S, Heid D, Janssen M, Renders S, Rohde C, Bauer M, Bruckmann M, Zinz R, Pauli C, Besenbeck B, Wickenhauser C, Trumpp A, Krijgsveld J, Müller-Tidow C, Blank MF.Protein tyrosine kinase 2b inhibition reverts niche-associated resistance to tyrosine kinase inhibitors in AML. Leukemia. 2022; 36(10):2418-2429. doi: 10.1038/s41375-022-01687-x.
Janssen M, Schmidt C, Bruch PM, Blank MF, Rohde C, Waclawiczek A, Heid D, Renders S, Göllner S, Vierbaum L, Besenbeck B, Herbst SA, Knoll M, Kolb C, Przybylla A, Weidenauer K, Ludwig AK, Fabre M, Gu M, Schlenk RF, Stölzel F, Bornhäuser M, Röllig C, Platzbecker U, Baldus C, Serve H, Sauer T, Raffel S, Pabst C, Vassiliou G, Vick B, Jeremias I, Trumpp A, Krijgsveld J, Müller-Tidow C, Dietrich S.Venetoclax synergizes with gilteritinib in FLT3 wild-type high-risk acute myeloid leukemia by suppressing MCL-1. Blood. 2022; 140(24):2594-2610. doi: 10.1182/blood.2021014241.
Meirow Y, Jovanovic M, Zur Y, Habib J, Colombo DF, Twaik N, Ashkenazi-Preiser H, Ben-Meir K, Mikula I Jr, Reuven O, Kariv G, Daniel L, Baraghithy S, Klein Y, Krijgsveld J, Levaot N, Baniyash M. Specific inflammatory osteoclast precursors induced during chronic inflammation give rise to highly active osteoclasts associated with inflammatory bone loss. Bone Res. 2022; 10(1):36. doi: 10.1038/s41413-022-00206-z.
Hisaoka M, Schott J, Bortecen T, Lindner D, Krijgsveld J, Stoecklin G.Preferential translation of p53 target genes. RNA Biol. 2022; 19(1):437-452. doi: 10.1080/15476286.2022.2048562
2021
Kalxdorf, M., T. Müller, O. Stegle and J. Krijgsveld. IceR improves proteome coverage and data completeness in global and single-cell proteomics. Nat Commun (2021), 12(1):4787. doi: 10.1038/s41467-021-25077-6. PMID: 34373457
Rafiee MR, Krijgsveld J. Using ChIP-SICAP to Identify Proteins That Co-localize in Chromatin. Methods Mol Biol. (2021), 2351:275-288. doi: 10.1007/978-1-0716-1597-3_15. PMID: 34382195
Bakr A, Hey J, Sigismondo G, Liu CS, Sadik A, Goyal A, Cross A, Iyer RL, Müller P, Trauernicht M, Breuer K, Lutsik P, Opitz CA, Krijgsveld J, Weichenhan D, Plass C, Popanda O, Schmezer P.ID3 promotes homologous recombination via non-transcriptional and transcriptional mechanisms and its loss confers sensitivity to PARP inhibition. Nucleic Acids Res. 2021 Nov 18;49(20):11666-11689. doi: 10.1093/nar/gkab964.
Singhal M, Gengenbacher N, Abdul Pari AA, Kamiyama M, Hai L, Kuhn BJ, Kallenberg DM, Kulkarni SR, Camilli C, Preuß SF, Leuchs B, Mogler C, Espinet E, Besemfelder E, Heide D, Heikenwalder M, Sprick MR, Trumpp A, Krijgsveld J, Schlesner M, Hu J, Moss SE, Greenwood J, Augustin HG., Temporal multi-omics identifies LRG1 as a vascular niche instructor of metastasis. Science Transl Med (2021), 13(609):eabe6805. doi: 10.1126/scitranslmed.abe6805. PMID: 34516824
Meyfour A, Pahlavan S, Mirzaei M, Krijgsveld J, Baharvand H, Salekdeh GH. The quest of cell surface markers for stem cell therapy. Cell Mol Life Sci. (2021), 78(2):469-495. doi: 10.1007/s00018-020-03602-y. PMID: 32710154
Launonen KM, Paakinaho V, Sigismondo G, Malinen M, Sironen R, Hartikainen JM, Laakso H, Visakorpi T, Krijgsveld J, Niskanen EA, Palvimo JJ. Chromatin-directed proteomics-identified network of endogenous androgen receptor in prostate cancer cells. Oncogene (2021), 40(27):4567-4579. doi: 10.1038/s41388-021-01887-2. PMID: 34127815
Strzeszewska-Potyrała A, Staniak K, Czarnecka-Herok J, Rafiee MR, Herok M, Mosieniak G, Krijgsveld J, Sikora E. Chromatin-Directed Proteomics Identifies ZNF84 as a p53-Independent Regulator of p21 in Genotoxic Stress Response. Cancers (Basel). (2021), 13(9):2115. doi: 10.3390/cancers13092115. PMID: 33925586
Morigny P, Kaltenecker D, Zuber J, Machado J, Mehr L, Tsokanos FF, Kuzi H, Hermann CD, Voelkl M, Monogarov G, Springfeld C, Laurent V, Engelmann B, Friess H, Zörnig I, Krüger A, Krijgsveld J, Prokopchuk O, Fisker Schmidt S, Rohm M, Herzig S, Berriel Diaz M. Association of circulating PLA2G7 levels with cancer cachexia and assessment of darapladib as a therapy. J Cachexia Sarcopenia Muscle. (2021). doi: 10.1002/jcsm.12758. Online ahead of print. PMID: 34427055
Kiehlmeier S, Rafiee MR, Bakr A, Mika J, Kruse S, Müller J, Schweiggert S, Herrmann C, Sigismondo G, Schmezer P, Krijgsveld J, Gröschel S. Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia. Leukemia. (2021), doi: 10.1038/s41375-021-01235-z. Online ahead of print. PMID: 33911178
Hoppe-Seyler K, Herrmann AL, Däschle A, Kuhn BJ, Strobel TD, Lohrey C, Bulkescher J, Krijgsveld J, Hoppe-Seyler F. Effects of Metformin on the virus/host cell crosstalk in human papillomavirus-positive cancer cells. Int J Cancer. (2021), 149(5):1137-1149 doi: 10.1002/ijc.33594. PMID: 33844847
Paakinaho V, Lempiäinen JK, Sigismondo G, Niskanen EA, Malinen M, Jääskeläinen T, Varjosalo M, Krijgsveld J, Palvimo JJ. SUMOylation regulates the protein network and chromatin accessibility at glucocorticoid receptor-binding sites. Nucleic Acids Res. (2021), 49(4):1951-1971. doi: 10.1093/nar/gkab032. PMID: 33524141
Zowada MK, Tirier SM, Dieter SM, Krieger TG, Oberlack A, Chua RL, Huerta M, Ten FW, Laaber K, Park J, Jechow K, Müller T, Kalxdorf M, Kriegsmann M, Kriegsmann K, Herbst F, Krijgsveld J, Schneider M, Eils R, Glimm H, Conrad C, Ball CR. Functional States in Tumor-Initiating Cell Differentiation in Human Colorectal Cancer. Cancers (Basel). (2021), 13(5):1097. doi: 10.3390/cancers13051097. PMID: 33806447
Ecker J, Thatikonda V, Sigismondo G, Selt F, Valinciute G, Oehme I, Müller C, Buhl JL, Ridinger J, Usta D, Qin N, van Tilburg CM, Herold-Mende C, Remke M, Sahm F, Westermann F, Kool M, Wechsler-Reya RJ, Chavez L, Krijgsveld J, Jäger N, Pfister SM, Witt O, Milde T. Reduced chromatin binding of MYC is a key effect of HDAC inhibition in MYC amplified medulloblastoma. Neuro Oncol. (2021), 23(2):226-239 doi: 10.1093/neuonc/noaa191. PMID: 32822486
Müller T, Boileau E, Talyan S, Kehr D, Varadi K, Busch M, Most P, Krijgsveld J, Dieterich C. Updated and enhanced pig cardiac transcriptome based on long-read RNA sequencing and proteomics. J Mol Cell Cardiol. (2021), 150:23-31. doi: 10.1016/j.yjmcc.2020.10.005. PMID: 33049256
2020
Müller T, Kalxdorf M, Longuespée R, Kazdal DN, Stenzinger A, Krijgsveld J. Automated sample preparation with SP3 for low-input clinical proteomics. Mol Syst Biol (2020); 16(1):e9111. https://doi.org/10.15252/msb.20199111
Bunina D, Abazova N, Diaz N, Noh K-M*, Krijgsveld J*, Zaugg JB*. Genomic rewiring of SOX2 chromatin interaction network during differentiation of ESCs to postmitotic neurons. *Joint senior authors. Cell Syst (2020), 10(6):480-494.e8. https://doi.org/10.1016/j.cels.2020.05.003
Selkrig J, Li N, Hausmann A, ManganM, Zietek M, Mateus A, Bobonis J, Sueki A, Imamura H, El Debs B, Sigismondo G, Florea BI, Overkleeft HS, Kopitar-Jerala N, Turk B, Beltrao P, Savitski M, Latz E, Hardt WD, Krijgsveld J*, Typas A*. Spatiotemporal proteomics uncovers cathepsin-dependent host cell death during bacterial infection. *Joint senior authors. Nat Microbiol (2020), 5(9):1119-1133. https://doi.org/10.1038/s41564-020-0736-7
Rafiee MR, Sigismondo G, Kalxdorf M, Förster L, Brügger B, Béthune J, Krijgsveld J. Protease-resistant streptavidin for interaction proteomics. Mol Syst Biol (2020), 16(5):e9370. https://doi.org/10.15252/msb.20199370
Kuhn TC, Knobel J, Burkert-Rettenmaier S, Li X, Meyer IS, Jungmann A, Sicklinger F, Backs J, Lasitschka F, Müller OJ, Katus HA, Krijgsveld J*, Leuschner F*. Secretome Analysis of Cardiomyocytes Identifies PCSK6 as a Novel Player in Cardiac Remodeling After Myocardial Infarction. *Joint senior authors. Circulation (2020); 141:1628–1644. https://doi.org/10.1161/circulationaha.119.044914
Müller T, Boileau E, Talyan S, Kehr D, Varadi K, Busch M, Most P, Krijgsveld J, Dieterich C. Updated and enhanced pig cardiac transcriptome based on long-read RNA sequencing and proteomics. J Mol Cell Cardiol (2020), 150:23-31. https://doi.org/10.1016/j.yjmcc.2020.10.005
Meyfour A, Pahlavan S, Mirzaei M, Krijgsveld J, Baharvand H, Salekdeh GH. The quest of cell surface markers for stem cell therapy. Cell Mol Life Sci. (2020). https://doi.org/10.1007/s00018-020-03602-y
Ecker J, Thatikonda V, Sigismondo G, Selt F, Valinciute G, Oehme I, Müller C, Buhl JL, Ridinger J, Usta D, Qin N, van Tilburg CM, Herold-Mende C, Remke M, Sahm F, Westermann F, Kool M, Wechsler-Reya RJ, Chavez L, Krijgsveld J, Jäger N, Pfister SM, Witt O, Milde T. Reduced chromatin binding of MYC is a key effect of HDAC inhibition in MYC amplified medulloblastoma. Neuro Oncol. (2020) https://doi.org/10.1093/neuonc/noaa191
Raffel S, Klimmeck D, Falcone M, Demir A, Pouya A, Zeisberger P, Lutz C, Tinelli M, Bischel O, Bullinger L, Ho AD, Müller-Tidow C, Gu Z, Hermann C, Krijgsveld J*, Trumpp A*, Hansson J*. Quantitative proteomics reveals specific metabolic features of Acute Myeloid Leukemia stem cells. *Joint senior authors. Blood (2020), 136(13):1507-1519. https://doi.org/10.1182/blood.2019003654
Delacher M, Barra MM, Herzig Y, Eichelbaum K, Rafiee M-R, Richards DM, Träger U, Hofer AC, Kazakov A, Braband KL, Gonzalez M, Wöhrl L, Schambeck K, Imbusch CD, Abramson J, Krijgsveld J, and Feuerer M. Quantitative proteomics identifies TCF1 as a negative regulator of Foxp3 expression in conventional T cells. iScience (2020), 23(5):101127. https://doi.org/10.1016/j.isci.2020.101127
Smith T, Villanueva E, Queiroz RML, Dawson CS, Elzek M, Urdaneta EC, Willis AE, Beckmann BM, Krijgsveld J, Lilley KS. Organic phase separation opens up new opportunities to interrogate the RNA-binding proteome. Curr Opin Chem Biol. (2020); 54:70-75. https://doi.org/10.1016/j.cbpa.2020.01.009
Pauli C, Liu Y, Rohde C, Cui C, Fijalkowska D, Gerloff D, Walter C, Krijgsveld J, Dugas M, Edemir B, Pabst C, Mueller LP, Zhou F, Müller-Tidow C. Site-specific methylation of 18S ribosomal RNA by SNORD42A is required for Acute Myeloid Leukemia cell proliferation. Blood (2020), 135(23):2059-2070. https://doi.org/10.1182/blood.2019004121
Carnesecchi J, Sigismondo G, Domsch K, Baader CEP, Rafiee MR, Krijgsveld J and Lohmann I. Multi-level and lineage-specific interactome of the Hox transcription factor Ubx contributes to its functional specificity. Nature Communications (2020), 11(1): 1388. https://doi.org/10.1038/s41467-020-15223-x
Plum T, Wang X, Rettel M, Krijgsveld J, Feyerabend TB, Rodewald HR. Human Mast Cell Proteome Reveals Unique Lineage, Putative Functions, and Structural Basis for Cell Ablation. Immunity (2020);52(2):404-
2019
Trendel J, Schwarzl T, Horos R, Prakash A, Bateman A, Hentze MW, Krijgsveld J. The Human RNA-Binding Proteome and Its Dynamics During Arsenite-Induced Translational Arrest. Cell (2019) 176(1-2):391-403. https://doi.org/10.1016/j.cell.2018.11.004
Cooke A, Schwarzl T, Huppertz I, Kramer G, Mantas P, Alleaume AM, Huber W, Krijgsveld J, Hentze MW. The RNA-Binding Protein YBX3 Controls Amino Acid Levels by Regulating SLC mRNA Abundance. Cell Rep. (2019); 27(11):3097-3106.e5. https://doi.org/10.1016/j.celrep.2019.05.039.
Hübner JM, Müller T, Papageorgiou DN, Mauermann M, Krijgsveld J, Russell RB, Ellison DW, Pfister SM, Pajtler KW, Kool M. EZHIP / CXorf67 mimics K27M mutated oncohistones and functions as an intrinsic inhibitor of PRC2 function in aggressive posterior fossa ependymoma. Neuro Oncol. (2019). pii: noz058. https://doi.org/10.1093/neuonc/noz058.
Lamberti MJ, Rettel M, Krijgsveld J, Rivarola VA, Rumie Vittar NB. Secretome profiling of heterotypic spheroids suggests a role of fibroblasts in HIF-1 pathway modulation and colorectal cancer photodynamic resistance. Cell Oncol (Dordr). (2019) https://doi.org/10.1007/s13402-018-00418-8.
Bossler F, Kuhn BJ, Günther T, Kraemer SJ, Khalkar P, Adrian S, Lohrey C, Holzer A, Shimobayashi M, Dürst M, Mayer A, Rösl F, Grundhoff A, Krijgsveld J, Hoppe-Seyler K, Hoppe-Seyler F. Repression of Human Papillomavirus Oncogene Expression under Hypoxia Is Mediated by PI3K/mTORC2/AKT Signaling. MBio. (2019) 10(1). pii: e02323-18. https://doi.org/10.1128/mBio.02323-18
Hughes C, Moggridge S, Müller T, Sorensen P, Morin G, and Krijgsveld J. Single-pot, solid-phase-enhanced sample preparation for proteomics experiments. Nature Protocols (2019) 14(1):68-85. https://doi.org/10.1038/s41596-018-0082-x
Cagnetta R, Wong H, Frese CK, Mallucci GR, Krijgsveld J, Holt CE. Noncanonical modulation of eIF2 pathway controls increase in local translation during neural wiring. Mol Cell (2019) 7;73(3):474-489 https://doi.org//10.1016/j.molcel.2018.11.013.
Erich K, Reinle K, Müller T, Munteanu B, Sammour DA, Hinsenkamp I, Gutting T, Burgermeister E, Findeisen P, Ebert MP, Krijgsveld J, Hopf C. Spatial distribution of endogenous tissue protease activity in gastric carcinoma mapped by MALDI mass spectrometry imaging. Mol Cell Proteomics (2019), 18(1):151-161. https://doi.org/10.1074/mcp.RA118.000980.
2018
Chang L, Azzolin L, Di Biagio D, Zanconato F, Battilana G, Lucon Xiccato R, Aragona M, Giulitti S, Panciera T, Gandin A, Sigismondo G, Krijgsveld J, Fassan M, Brusatin G, Cordenonsi M, Piccolo S. The SWI/SNF complex is a mechanoregulated inhibitor of YAP and TAZ. Nature (2018), 563(7730):265-269.
Zanconato F, Battilana G, Forcato M, Filippi L, Azzolin L, Manfrin A, Quaranta E, Di Biagio D, Sigismondo G, Guzzardo V, Lejeune P, Haendler B, Krijgsveld J, Fassan M, Bicciato S, Cordenonsi M, Piccolo S. Transcriptional addiction in cancer cells is mediated by YAP/TAZ through BRD4. Nature Med. (2018), 24(10):1599-1610.
Ali Khan A, Hansson J, Weber P, Foehr S, Krijgsveld J, Herzig S, Scheideler M. Comparative secretome analyses of primary murine white and brown adipocytes reveal novel adipokines. Mol Cell Proteomics. (2018), 17:2358-2370. https://doi.org/10.1074/mcp.RA118.000704
Cagnetta R, Frese CK, Shigeoka T, Krijgsveld J*, Holt CE*. Rapid cue-specific remodeling of the nascent axonal proteome. *Joint senior authors, Neuron (2018), 99(1): 29–46
Dewari PS, Southgate B, Mccarten K, Monogarov G, O'Duibhir E, Quinn N, Tyrer A, Leitner MC, Plumb C, Kalantzaki M, Blin C, Finch R, Bressan RB, Morrison G, Jacobi AM, Behlke MA, von Kriegsheim A, Tomlinson S, Krijgsveld J, Pollard SM. An efficient and scalable pipeline for epitope tagging in mammalian stem cells using Cas9 ribonucleoprotein.
Elife. (2018) ;7. pii: e35069.
Buczak K, Ori A, Kirkpatrick JM, Holzer K, Dauch D, Roessler S, Endris V, Lasitschka F, Parca L, Schmidt A, Zender L, Schirmacher P, Krijgsveld J, Singer S, Beck M. Spatial Tissue Proteomics Quantifies Inter- and Intratumor Heterogeneity in Hepatocellular Carcinoma (HCC).
Molecular and Cellular Proteomics. (2018);17(4):810-825.
2017
Castello A, Frese CK, Fischer B, Järvelin AI, Horos R, Alleaume AM, Foehr S, Curk T, Krijgsveld J, Hentze MW. Identification of RNA-binding domains of RNA-binding proteins in cultured cells on a system-wide scale with RBDmap. Nat Protoc. (2017); 12(12):2447-2464
Raffel S, Falcone M, Kneisel N, Hansson J, Wang W, Lutz C, Bullinger L, Poschet G, Nonnenmacher Y, Barnert A, Bahr C, Zeisberger P, Przybylla A, Sohn M, Tönjes M, Erez A, Adler L, Jensen P, Scholl C, Fröhling S, Cocciardi S, Wuchter P, Thiede C, Flörcken A, Westermann J, Ehninger G, Lichter P, Hiller K, Hell R, Herrmann C, Ho AD, Krijgsveld J, Radlwimmer B, Trumpp A. BCAT1 restricts αKG levels in AML stem cells leading to IDHmut-like DNA hypermethylation. Nature (2017); 551(7680):384-388
Abazova N, Krijgsveld J. Advances in stem cell proteomics. Curr Opin Genet Dev. (2017);46:149-155
Nötzold L, Frank L, Gandhi M, Polycarpou-Schwarz M, Groß M, Gunkel M, Beil N, Erfle H, Harder N, Rohr K, Trendel J, Krijgsveld J, Longerich T, Schirmacher P, Boutros M, Erhardt S, Diederichs S. The long non-coding RNA LINC00152 is essential for cell cycle progression through mitosis in HeLa cells. Sci Rep. (2017);7(1):2265
Rogell B, Fischer B, Rettel M, Krijgsveld J, Castello A, Hentze MW. Specific RNP capture with antisense LNA/DNA mixmers. RNA. (2017);23(8):1290-1302
Okawa S, Gagrica S, Blin C, Ender C, Pollard SM, Krijgsveld J. Proteome and Secretome Characterisation of Glioblastoma-derived Neural Stem Cells. Stem Cells. (2017); 35(4):967-980
Mueller T, Winter D: Systematic Evaluation of Protein Reduction and Alkylation Reveals Massive Unspecific Side Effects by Iodine-containing Reagents. Molecular and Cellular Proteomics 16 (7), 1173-1187, 2017
2016
Kramer G, Krijgsved J. Turning Over Paradigms in Protein Decay. Dev Cell (2016);39(3):284-285
Rafiee MR, Girardot C, Sigismondo G, Krijgsved J. Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins. Mol Cell. (2016);64(3):624-635
Liao Y, Castello A, Fischer B, Leicht S, Föehr S, Frese CK, Ragan C, Kurscheid S, Pagler E, Yang H, Krijgsved J, Hentze MW, Preiss T. The Cardiomyocyte RNA-Binding Proteome: Links to Intermediary Metabolism and Heart Disease. Cell Reports (2016);16(5):1456-69
Castello A, Fischer B, Frese CK, Horos R, Alleaume AM, Foehr S, Curk T, Krijgsved J, Hentze MW. Comprehensive Identification of RNA-Binding Domains in Human Cells. Mol Cell (2016), 63(4): 696–710
Sysoev VO, Fischer B, Frese CK, Gupta I, Krijgsved J, Hentze MW, Castello A, Ephrussi A. Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila. Nat Commun. (2016), 7:12128
Schaefer M, Oeing CU, Rohm M, Baysal-Temel E, Lehmann LH, Bauer R, Volz HC, Boutros M, Sohn D, Sticht C, Gretz N, Eichelbaum K, Werner T, Hirt MN, Eschenhagen T, Müller-Decker K, Strobel O, Hackert T, Krijgsveld J, Katus HA, Berriel Diaz M, Backs J, Herzig S: Ataxin-10 is part of a cachexokine cocktail triggering cardiac metabolic dysfunction in cancer cachexia. Molecular Metabolism 5 (2), 67-78, 2016
Virant-Klun I, Leicht S, Hughes C, Krijgsved J. Identification of maturation-specific proteins by single-cell proteomics of human oocytes. Mol Cell Proteomics. (2016), 15(8):2616-27
Liepelt A, Naarmann-de Vries IS, Simons N, Eichelbaum K, Foehr S, Archer SK, Castello A, Usadel B, Krijgsved J, Preiss T, Marx G, Hentze MW, Ostareck DH, Ostareck-Lederer A. Identification of RNA-binding proteins in macrophages by interactome capture. Mol Cell Proteomics (2016), 15(8):2699-714
Sieber J, Hauer C, Bhuvanagiri M, Leicht S, Krijgsveld J, Neu-Yilik G, Hentze MW, Kulozik AE. Proteomic analysis reveals branch-specific regulation of the unfolded protein response by nonsense-mediated mRNA decay. Mol. Cell. Proteomics (2016), 15(5):1584-97
Vargel Ö, Zhang Y, Kosim K, Ganter K, Foehr S, Mardenborough Y, Shvartsman M, Enright AJ, Krijgsveld J, Lancrin C. Activation of the TGFβ pathway impairs endothelial to haematopoietic transition. Sci. Rep. (2016), 6:21518
Haberkant P, Stein F, Höglinger D, Gerl MJ, Brügger B, Van Veldhoven PP, Krijgsveld J, Gavin AC, Schultz C. Bifunctional Sphingosine for Cell-Based Analysis of Protein-Sphingolipid Interactions. ACS Chem Biol. (2016) 11(1):222-30
Dunne M, Leicht S, Krichel B, Mertens HD, Thompson A, Krijgsveld J, Svergun DI, Gómez-Torres N, Garde S, Uetrecht C, Narbad A, Mayer MJ, Meijers R. Crystal Structure of the CTP1L Endolysin Reveals How Its Activity Is Regulated by a Secondary Translation Product. J Biol Chem. (2016), 291(10):4882-93
Castello A, Horos R, Strein C, Fischer B, Eichelbaum K, Steinmetz LM, Krijgsveld J, Hentze MW: Comprehensive Identification of RNA-Binding Proteins by RNA Interactome Capture. Methods in Molecular Biology 1358, 131-139, 2016
2015
Schäfer M, Oeing CU, Rohm M, Baysal-Temel E, Lehmann LH, Bauer R, Volz HC, Boutros M, Sohn D, Sticht C, Gretz N, Eichelbaum K, Werner T, Hirt MN, Eschenhagen T, Müller-Decker K, Strobel O, Hackert T, Krijgsveld J, Katus HA, Berriel Diaz M, Backs J, Herzig S. Ataxin-10 is part of a cachexokine cocktail triggering cardiac metabolic dysfunction in cancer cachexia. Mol Metab. (2015), 5:67-78.
Beckmann BM, Horos R, Fischer B, Castello A, Eichelbaum K, Alleaume AM, Schwarzl T, Curk T, Foehr S, Huber W, Krijgsveld J, Hentze MW. The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs. Nat Commun. (2015), 6:10127.
Castello A, Horos R, Strein C, Fischer B, Eichelbaum K, Steinmetz LM, Krijgsveld J, Hentze MW. Comprehensive Identification of RNA-Binding Proteins by RNA Interactome Capture. Methods Mol Biol. 2016;1358:131-9
Barra MM, Richards DM, Hansson J, Hofer AC, Delacher M, Hettinger J, Krijgsveld J, Feuerer M. Transcription Factor 7 Limits Regulatory T Cell Generation in the Thymus. J Immunol. (2015), 195(7):3058-70
Haas S, Hansson J, Klimmeck D, Loeffler D, Velten L, Uckelmann H, Wurzer S, Prendergast AM, Schnell A, Hexel K, Santarella-Mellwig R, Blaszkiewicz S, Kuck A, Geiger H, Milsom MD, Steinmetz LM, Schroeder T, Trumpp A, Krijgsveld J, Essers MA. Inflammation-Induced Emergency Megakaryopoiesis Driven by Hematopoietic Stem Cell-like Megakaryocyte Progenitors. Cell Stem Cell. (2015), 17(4):422-34
2014
Bhuvanagiri M, Lewis J, Putzker K, Becker JP, Leicht S, Krijgsveld J, Batra R, Turnwald B, Jovanovic B, Hauer C, Sieber J, Hentze MW, Kulozik AE. 5-azacytidine inhibits nonsense-mediated decay in a MYC-dependent fashion. EMBO Mol Med. (2014) 6(12):1593-609
Klimmeck D, Cabezas-Wallscheid N, Reyes A, Von Paleske L, Renders S, Hansson J, Krijgsveld J, Huber W, Trumpp A. Transcriptome-wide Profiling and Posttranscriptional Analysis of Hematopoietic Stem/Progenitor Cell Differentiation toward Myeloid Commitment. Stem Cell Reports (2014), 3(5):858–875
Kronja I, Whitfield ZJ, Yuan B, Dzeyk K, Kirkpatrick J, Krijgsveld J, Orr-Weaver TL. Quantitative proteomics reveals the dynamics of protein changes during Drosophila oocyte maturation and the oocyte-to-embryo transition. PNAS (2014); 111(45):16023-8
Hughes C, Foehr S, Garfield DA, Furlong EE, Steinmetz LM, Krijgsveld J, Ultrasensitive proteome analysis using paramagnetic bead technology.Molecular Systems Biology (2014); 10: 757 Highlighted in 'News and Views' by Kanshin and Thibault, Molecular Systems Biology (2014); 10: 758
Cabezas-Wallscheid N, Klimmeck D, Hansson J, Lipka DB, Reyes A, Wang Q, Weichenhan D, Lier A, von Paleske L, Renders S, Wünsche P, Zeisberger P, Brocks D, Gu L, Herrmann C, Haas S, Essers MA, Brors B, Eils R, Huber W*, Milsom MD*, Plass C*, Krijgsveld J*, Trumpp A*. Identification of Regulatory Networks in HSCs and Their Immediate Progeny via Integrated Proteome, Transcriptome, and DNA Methylome Analysis. *Joint last author Cell Stem Cell (2014), 15(4):507-22
Eichelbaum K and Krijgsveld J. Combining Pulsed SILAC Labeling and Click-Chemistry for Quantitative Secretome Analysis. Methods Mol Biol. (2014), 1174:101-14.
Kronja I, Yuan B, Eichhorn SW, Dzeyk K, Krijgsveld J, Bartel DP, Orr-Weaver TL. Widespread Changes in the Posttranscriptional Landscape at the Drosophila Oocyte-to-Embryo Transition. Cell Reports (2014), 7(5):1495-508
Eichelbaum K and Krijgsveld J Rapid temporal dynamics of transcription, protein synthesis and secretion during macrophage activation. Mol Cell Proteomics (2014), 13(3):792-810
Virant-Klun I. and Krijgsveld J (2014). Proteomes of animal oocytes: what can we learn for human oocytes in the in vitro fertilization programme? BioMed Research International, (2014), 2014:856907. doi: 10.1155/2014/856907
Gonzalez D, Hamidi N, Del Sol R, Benschop JJ, Nancy T, Li C, Francis L, Tzouros M, Krijgsveld J, Holstege FCP, and Conlan RS. Suppression of Mediator is regulated by Cdk8-dependent Grr1 turnover of the Med3 coactivator. PNAS, (2014), 111(7):2500-5
Polonio-Vallon T, Kirkpatrick J, Krijgsveld J, and Hofmann TG. Src kinase modulates the apoptotic p53 pathway by altering HIPK2 localization. Cell Cycle (2014), 13(1):115-25
2013
Yokoyama H, Nakos K, Santarella-Mellwig R, Rybina S, Krijgsveld J, Koffa MD, and Mattaj IW (2013). CHD4 Is a RanGTP-Dependent MAP that Stabilizes Microtubules and Regulates Bipolar Spindle Formation. Curr Biol. 23(24):2443-51
Hettinger J, Richards D, Hansson J, Barra MM, Krijgsveld J, and Feuerer M (2013). Identification of a monocyte/macrophage-restricted progenitor in the bone marrow. Nature Immunology 14(8):821-30.
Kwon SC, Yi H, Eichelbaum K, Föhr S, Fischer B, You KT, Castello A, Krijgsveld J, Hentze MW, and Kim VN (2013).The RNA-binding protein repertoire of embryonic stem cells. Nat Struct Mol Biol. 20(9):1122-30
Hansson, J. and Krijgsveld, J (2013). Proteomic analysis of cell fate decision. Curr Opin Genet Dev. 23(5):540-7
Okawa S, Fischer B, Krijgsveld J (2013). Properties of isotope patterns and their utility for peptide identification in large-scale proteomic experiments. Rapid Commun Mass Spectrom 15;27(9):1067-75.
Castello A, Horos R, Strein C, Fischer B, Eichelbaum K, Steinmetz LM, Krijgsveld J, Hentze MW (2013). System-wide identification of RNA-binding proteins by interactome capture. Nature Protocols 8(3):491-500
Dastidar EG, Dzeyk K, Krijgsveld J, Malmquist NA, Doerig C, Scherf A, Lopez-Rubio JJ. (2013). Comprehensive histone phosphorylation analysis and identification of Pf14-3-3 protein as a histone H3 phosphorylation reader in malaria parasites. PLoS One 8(1):e53179
2012
Eichelbaum K, Winter M, Diaz MB, Herzig S, Krijgsveld J (2012). Selective enrichment of newly synthesized proteins for quantitative secretome analysis. Nature Biotechnology 30(10):984-90
Hansson J, Rafiee MR, Reiland S, Polo JM, Gehring J, Okawa S, Huber W, Hochedlinger K, Krijgsveld J (2012). Highly coordinated proteome dynamics during reprogramming of somatic cells to pluripotency. Cell Reports 2(6):1579-92
Castello A, Fischer B, Schuschke K, Horos R, Beckmann B, Strein C, Humphreys DT, Preiss T, Steinmetz L, Krijgsveld J* and Hentze MW* (2012). Insights into RNA biology from a mammalian cell mRNA interactome. Cell 149(6):1393-406. *Joint last author
Hughes C, Krijgsveld J (2012). Developments in quantitative mass spectrometry for the analysis of proteome dynamics. Trends Biotechnol. 30(12):668-76.
Klimmeck D.**, Hansson J.**, Raffel S., Vakhrushev S., Trumpp A.* and Krijgsveld J.* (2012). Proteomic cornerstones of multipotent hematopoietic stem and progenitor cells. Mol Cell Proteomics 11(8):286-302. ** Joint first author, *Joint last author
Gouw JW, Krijgsveld J (2012). MSQuant: a platform for stable isotope-based quantitative proteomics. Methods Mol Biol. 2012;893:511-22.
Van Hoof D, Krijgsveld J, Mummery C. Proteomic analysis of stem cell differentiation and early development (2012). Cold Spring Harb Perspect Biol. 4(3) pii: a008177 (doi: 10.1101/cshperspect.a008177)